Experimental evolution for cell biology

Helsen, Jana; Sherlock, Gavin; Dey, G.K.

doi:10.1016/j.tcb.2023.04.006

Cited by 4 publications

(2 citation statements)

References 56 publications

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“…6h ), we believe that it can be a future model for cell biology for understanding how typically essential processes function in the absence of key cell cycle regulators. Moreover, framing future studies within an evolutionary cell biology framework ( Helsen et al . 2023 ) will aid in understanding the biochemical and molecular details of the evolution of core histone gene regulation in Hanseniaspora and budding yeast more broadly.…”

Section: Discussionmentioning

confidence: 99%

Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum

Haase,

Steenwyk,

Boeke

2024

Genetics

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Core histone genes display a remarkable diversity of cis-regulatory mechanisms despite their protein sequence conservation. However, the dynamics and significance of this regulatory turnover are not well understood. Here we describe the evolutionary history of core histone gene regulation across 400 million years in budding yeasts. We find that canonical mode of core histone regulation – mediated by the trans-regulator Spt10 – is ancient, likely emerging between 320-380 million years ago and is fixed in the majority of extant species. Unexpectedly, we uncovered the emergence of a novel core histone regulatory mode in the Hanseniaspora genus, from its fast-evolving lineage (FEL), which coincided with the loss of one copy of its paralogous core histones genes. We show that the ancestral Spt10 histone regulatory mode was replaced, via cis-regulatory changes in the histone control regions, by a derived Mcm1 histone regulatory mode and that this rewiring event occurred with no changes to the trans-regulator, Mcm1, itself. Finally, we studied the growth dynamics of the cell cycle and histone synthesis in genetically modified Hanseniaspora uvarum. We find that H. uvarum divides rapidly, with most cells completing a cell cycle within 60 minutes. Interestingly, we observed that the regulatory coupling between histone and DNA synthesis was lost in H. uvarum. Our results demonstrate that core histone gene regulation was fixed anciently in budding yeasts, however it has greatly diverged in the Hanseniaspora FEL.

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Section: Discussionmentioning

confidence: 99%

Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum

Haase,

Steenwyk,

Boeke

2024

Genetics

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“…Given the uniqueness of genes absent from the Hanseniaspora FEL, we believe it can be a future model for cell biology for understanding how typically essential processes function in the absence of key cell cycle regulators. Moreover, framing future studies into an evolutionary cell biology framework (Helsen et al . 2023) will enhance future studies into the biochemical and molecular details of core histone gene regulation in Hanseniaspora and budding yeast more broadly.…”

Section: Discussionmentioning

confidence: 99%

Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeastHanseniaspora uvarum

Haase,

Steenwyk,

Boeke

2023

Preprint

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Across eukaryotic species, core histone genes display a remarkable diversity of cis-regulatory mechanisms despite their protein sequence conservation. However, the dynamics and significance of this regulatory turnover are not well understood. Here we describe the evolutionary history of core histone gene regulation across 400 million years in Saccharomycotina yeasts, revealing diverse lineage-specific solutions to core histone expression. We further characterize the emergence of a novel regulatory mode in the Hanseniaspora genus, which coincided with the loss of one copy of its paralogous core histones genes from its fast-evolving lineage. By analyzing the growth dynamics using live cell imaging of genetically modified Hanseniaspora uvarum, we observed a regulatory decoupling of core histone synthesis from DNA synthesis and propose that this may be adaptive for its rapid cell cycle progression. Overall, our findings imply that the frequent turnover of core histone cis-regulatory mechanisms likely provides distinct adaptive solutions for specific life histories.

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Mutagenesis techniques for evolutionary engineering of microbes – exploiting CRISPR-Cas, oligonucleotides, recombinases, and polymerases

Zimmermann,

Prieto-Vivas,

Voordeckers

et al. 2024

Trends in Microbiology

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Experimental evolution for cell biology

Cited by 4 publications

References 56 publications

Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum

Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum

Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeastHanseniaspora uvarum

Mutagenesis techniques for evolutionary engineering of microbes – exploiting CRISPR-Cas, oligonucleotides, recombinases, and polymerases

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